That mineshaft thing's just weird. Maybe the superclass's decorator (which is probably called somewhere) is ignoring the setting and looking at its own base worldprovider?
Enabling/disabling levels and configuring the order? Sounds a little complex, but doable. I'll try to add it.
And I can make my ores configurable, and will, but the vanilla oregen that just won't go away are another matter. It's kind of like those mineshafts.
Ok, so there is a new bug I found. Upon loading the world, there are 20 seconds (exactly 20 seconds) lag in world loading. TPS goes down to zero for 20 seconds, the world has loaded chunks in 1 chunk radius around the player and that's all, you can't do anything. After 20 seconds of this freeze, chat produces a message "Failed to get the latest version from the server. Check your internet connection.". I managed to track it down to Deeper Caves.
By deleting mods one by one and running the game and starting a map over and over again.
Can you fix at least this? Because if there are hostile mobs around the player during this lagging event - player dies, because game compansates lag with time travel of some sort - events happen quickier than they should.